1ZZN

Crystal structure of a group I intron/two exon complex that includes all catalytic metal ion ligands.

• PDB DOI:  https://doi.org/10.2210/pdb1ZZN/pdb
• NAKB: 1ZZN

• Classification: STRUCTURAL PROTEIN/RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-06-14 Released: 2005-08-30 
• Deposition Author(s): Stahley, M.R., Strobel, S.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.37 Å
• R-Value Free: 0.307 
• R-Value Work: 0.269 
• R-Value Observed: 0.269 

Literature

Structural evidence for a two-metal-ion mechanism of group I intron splicing.

Stahley, M.R., Strobel, S.A.

(2005) Science 309: 1587-1590

• PubMed: 16141079 
• DOI: https://doi.org/10.1126/science.1114994
• Primary Citation of Related Structures:  
  1ZZN


• PubMed Abstract: 
  

We report the 3.4 angstrom crystal structure of a catalytically active group I intron splicing intermediate containing the complete intron, both exons, the scissile phosphate, and all of the functional groups implicated in catalytic metal ion coordination, including the 2'-OH of the terminal guanosine. This structure suggests that, like protein phosphoryltransferases, an RNA phosphoryltransferase can use a two-metal-ion mechanism. Two Mg2+ ions are positioned 3.9 angstroms apart and are directly coordinated by all six of the biochemically predicted ligands. The evolutionary convergence of RNA and protein active sites on the same inorganic architecture highlights the intrinsic chemical capacity of the two-metal-ion catalytic mechanism for phosphoryl transfer.

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Related Citations: 

• Crystal Structure of a Self-Splicing Group I Intron with Both Exons
  Adams, P.L., Stahley, M.R., Kosek, A.B., Wang, J., Strobel, S.A.
  (2004) Nature 430: 45

• Crystal Structure of a group I intron splicing intermediate
  Adams, P.L., Stahley, M.R., Gill, M.L., Kosek, A.B., Wang, J., Strobel, S.A.
  (2004) RNA 10: 1867

• In vitro splicing of the ribosomal RNA precursor of tetrahymena: involvement of a guanosine nucleotide in the excision of intervening sequence
  Cech, T.R., Zaug, A.J., Grabowaski, P.J.
  (1981) Cell 27: 487

• Self-splicing intron in tRNA genes of widely divergent bacteria
  Reinhold-Hurek, B., Shub, D.A.
  (1992) Nature 357: 173

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520-8114, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 83.51 kDa 
• Atom Count: 5,603 
• Modelled Residue Count: 317 
• Deposited Residue Count: 320 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A RNA BINDING DOMAIN	D [auth A]	98	Homo sapiens	Mutation(s): 2  Gene Names: SNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens) Explore P09012  Go to UniProtKB:  P09012
PHAROS:  P09012

Entity ID: 1
Molecule	Chains	Length	Organism	Image
197-MER	A [auth B]	197	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*AP*GP*AP*CP*GP*GP*CP*C)-3'	B [auth C]	22	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-R(*CP*AP*(5MU))-3'	C [auth D]	3	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	G [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	E [auth B], F [auth B], H [auth B], I [auth B], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.37 Å
• R-Value Free: 0.307 
• R-Value Work: 0.269 
• R-Value Observed: 0.269 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.466	α = 90
b = 108.466	β = 90
c = 246.4	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-30 
Deposition Author(s): Stahley, M.R., Strobel, S.A.

Revision History  

• Version 1.0: 2005-08-30
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Advisory, Refinement description
• Version 1.4: 2021-10-20
  Changes: Advisory, Database references, Derived calculations
• Version 1.5: 2023-08-23
  Changes: Data collection, Refinement description